title: Genome-wide copy number variations inferred from SNP genotyping arrays using a Large White and Minzhu intercross population.
abstract: Copy number variations (CNVs) are one of the main contributors to genetic diversity in animals and are broadly distributed in the genomes of swine. Investigating the performance and evolutionary impacts of pig CNVs requires comprehensive knowledge of their structure and function within and between breeds. In the current study, 4 different programs (i.e., GADA, PennCNV, QuantiSNP, and cnvPartition) were used to analyze Porcine SNP60 genotyping data of 585 pigs from one Large White × Minzhu intercross population to detect copy number variant regions (CNVRs). Overlapping CNVRs recalled by at least 2 programs were used to construct a powerful and comprehensive CNVR map, which contained 249 CNVRs (i.e., 70 gains, 43 losses, and 136 gains/losses) and covered 26.22% of the regions in the swine genome. Ten CNVRs, representing different predicted statuses, were selected for validation via quantitative real-time PCR (QPCR); 9/10 CNVRs (i.e., 90%) were validated. When being traced back to the F0 generation, 58 events were identified in only Minzhu F0 parents and 2 events were identified in only Large White F0 parents. A series of CNVR function analyses were performed. Some of the CNVRs functions were predicted, and several interesting CNVRs for meat quality traits and hematological parameters were obtained. A comprehensive and lower false rate genome-wide CNV map was constructed for Large White and Minzhu pig genomes in this study. Our results may provide an important basis for determining the relationship between CNVRs and important qualitative and quantitative traits. In addition, it can help to further understand genetic processes in pigs.
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
authors.forename: Ligang
authors.initials: L
authors.lastname: Wang
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Longchao
authors.initials: L
authors.lastname: Zhang
authors.forename: Hua
authors.initials: H
authors.lastname: Yan
authors.forename: Weizhen
authors.initials: W
authors.lastname: Luo
authors.forename: Jing
authors.initials: J
authors.lastname: Liang
authors.forename: Duxue
authors.initials: D
authors.lastname: Cheng
authors.forename: Shaokang
authors.initials: S
authors.lastname: Chen
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Ma
authors.forename: Xin
authors.initials: X
authors.lastname: Song
authors.forename: Kebin
authors.initials: K
authors.lastname: Zhao
authors.forename: Lixian
authors.initials: L
authors.lastname: Wang
mesh_terms: D000818:Animals; D056915:DNA Copy Number Variations / Q000235:genetics*; D005260:Female; D023281:Genomics; D060005:Genotyping Techniques; D006824:Hybridization, Genetic; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D013552:Swine / Q000235:genetics*